All Figures

	Figure 1: The density ( left panel) and temperature ( right panel) contours of four time snapshots of the hydrodynamical simulation. Time progresses from left to right, top to bottom at . In the right panel, contour lines refer to the dust temperature, while the color scale denotes the gas temperature.
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In the text

	Figure 2: The time evolution in the luminosity of the central source in the hydrodynamical simulation. This figure compares with Fig. 7 in Yorke & Bodenheimer (1999).
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In the text

	Figure 3: Trace particle motion in the hydrodynamical simulation. The particles are color-coded according to their initial radial position. Contour lines describe the density. The vertical color bar shows the particles initial distance from the center. The four panels ( from the top-left to bottom-right) show the particle positions at t=0.0, 0.5, 1.5, and 2.5  .
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In the text

	Figure 4: This figure shows the abundance distribution of Model 1. The top panel shows the radial abundance profile through the mid-plane of the disk. The bottom panel shows the spatial abundance distribution. The shaded area is where molecules are frozen out. The unit on the y-axis of the top panel is fractional abundance.
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In the text

	Figure 5: Abundance distribution of Model 2. Otherwise identical to 4.
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In the text

	Figure 6: Abundance distribution of Model 3. Otherwise similar to 4.
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In the text

	Figure 7: Abundance distribution of Model 3 without cosmic ray desorption and the default binding energy of 960 K. Otherwise similar to 4.
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In the text

	Figure 8: Abundance distribution of Model 3, including cosmic rays, but with a CO binding energy of 1740 K. Otherwise similar to 4.
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In the text

	Figure 9: The global fractional depletion in the various models. The small bump in the curves around 0.5 is due to a change in the luminosity output of the central source as the disk is formed.
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In the text

	Figure 10: In this plot, we show the abundance as a function of envelope mass. Also shown in this plot are data points taken from Jørgensen et al. (2005,2002). The open symbols are Class I objects, the filled diamonds are Class 0 sources and the filled squares are pre-stellar cores.
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In the text

	Figure 11: CO gas column densities of the models discussed in this paper. These profiles are observed through a pencil beam, and need to be convolved with an appropriate beam to be directly compared with observations.
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In the text

	Figure 12: Same as Fig. 11 but for CO ice column densities.
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In the text

	Figure 13: Time series of CO 3-2 spectra. The top three panels show the three different abundance models. The three lower panels show model 3, including cosmic ray desorption using three different binding energies. Time is shown by increasing line thickness and the four lines correspond to the four adopted time snapshots (0.0, 0.5, 1.5, and 2.5  ). Each line has been offset by 0.5 K.
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In the text

	Figure 14: Similar to Fig. 13 but for C18O 3-2.
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In the text

	Figure 15: Time series of CO and C18O spectra with a constant abundance profile. Time is represented by increasing line thickness.
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In the text